Biomolecular Concepts最新文献_第4页

Setting up multicolour TIRF microscopy down to the single molecule level. 设置多色TIRF显微镜到单分子水平。

Biomolecular Concepts Pub Date : 2023-01-01 DOI: 10.1515/bmc-2022-0032

Chiara Schirripa Spagnolo, Stefano Luin

{"title":"Setting up multicolour TIRF microscopy down to the single molecule level.","authors":"Chiara Schirripa Spagnolo, Stefano Luin","doi":"10.1515/bmc-2022-0032","DOIUrl":"https://doi.org/10.1515/bmc-2022-0032","url":null,"abstract":"Investigating biological mechanisms in ever greater detail requires continuous advances in microscopy techniques and setups. Total internal reflection fluorescence (TIRF) microscopy is a well-established technique for visualizing processes on the cell membrane. TIRF allows studies down to the single molecule level, mainly in single-colour applications. Instead, multicolour setups are still limited. Here, we describe our strategies for implementing a multi-channel TIRF microscopy system capable of simultaneous two-channel excitation and detection, starting from a single-colour commercial setup. First, we report some applications at high molecule density and then focus on the challenges we faced for achieving the single molecule level simultaneously in different channels, showing that rigorous optimizations on the setup are needed to increase its sensitivity up to this point, from camera setting to background minimization. We also discuss our strategies regarding crucial points of fluorescent labelling for this type of experiment: labelling strategy, kind of probe, efficiency, and orthogonality of the reaction, all of which are aspects that can influence the achievable results. This work may provide useful guidelines for setting up advanced single-molecule multi-channel TIRF experiments to obtain insights into interaction mechanisms on the cell membrane of living cells.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9813081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Dipalmitoyl-phosphatidylserine-filled cationic maltodextrin nanoparticles exhibit enhanced efficacy for cell entry and intracellular protein delivery in phagocytic THP-1 cells. 双棕榈酰磷脂酰丝氨酸填充的阳离子麦芽糖糊精纳米颗粒在吞噬THP-1细胞中表现出增强的细胞进入和细胞内蛋白质递送的功效。

Biomolecular Concepts Pub Date : 2023-01-01 DOI: 10.1515/bmc-2022-0029

Clément Brinkhuizen, Damien Shapman, Alexis Lebon, Magalie Bénard, Meryem Tardivel, Laurent Dubuquoy, Ludovic Galas, Rodolphe Carpentier

{"title":"Dipalmitoyl-phosphatidylserine-filled cationic maltodextrin nanoparticles exhibit enhanced efficacy for cell entry and intracellular protein delivery in phagocytic THP-1 cells.","authors":"Clément Brinkhuizen, Damien Shapman, Alexis Lebon, Magalie Bénard, Meryem Tardivel, Laurent Dubuquoy, Ludovic Galas, Rodolphe Carpentier","doi":"10.1515/bmc-2022-0029","DOIUrl":"https://doi.org/10.1515/bmc-2022-0029","url":null,"abstract":"Vaccination through the upper respiratory tract is a promising strategy, and particulate antigens, such as antigens associated with nanoparticles, triggered a stronger immune response than the sole antigens. Cationic maltodextrin-based nanoparticles loaded with phosphatidylglycerol (NPPG) are efficient for intranasal vaccination but non-specific to trigger immune cells. Here we focused on phosphatidylserine (PS) receptors, specifically expressed by immune cells including macrophages, to improve nanoparticle targeting through an efferocytosis-like mechanism. Consequently, the lipids associated with NPPG have been substituted by PS to generate cationic maltodextrin-based nanoparticles with dipalmitoyl-phosphatidylserine (NPPS). Both NPPS and NPPG exhibited similar physical characteristics and intracellular distribution in THP-1 macrophages. NPPS cell entry was faster and higher (two times more) than NPPG. Surprisingly, competition of PS receptors with phospho-L-serine did not alter NPPS cell entry and annexin V did not preferentially interact with NPPS. Although the protein association is similar, NPPS delivered more proteins than NPPG in cells. On the contrary, the proportion of mobile nanoparticles (50%), the movement speed of nanoparticles (3 µm/5 min), and protein degradation kinetics in THP-1 were not affected by lipid substitution. Together, the results indicate that NPPS enter cells and deliver protein better than NPPG, suggesting that modification of the lipids of cationic maltodextrin-based nanoparticles may be a useful strategy to enhance nanoparticle efficacy for mucosal vaccination.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9686476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The effects of supplementation of Nannochloropsis oculata microalgae on biochemical, inflammatory and antioxidant responses in diabetic rats. 补充纳米绿藻对糖尿病大鼠生化、炎症和抗氧化反应的影响。

Biomolecular Concepts Pub Date : 2022-10-31 eCollection Date: 2022-01-01 DOI: 10.1515/bmc-2022-0025

Ali Fereidouni, Ali Khaleghian, Neda Mousavi-Niri, Nasrollah Moradikor

{"title":"The effects of supplementation of Nannochloropsis oculata microalgae on biochemical, inflammatory and antioxidant responses in diabetic rats.","authors":"Ali Fereidouni, Ali Khaleghian, Neda Mousavi-Niri, Nasrollah Moradikor","doi":"10.1515/bmc-2022-0025","DOIUrl":"https://doi.org/10.1515/bmc-2022-0025","url":null,"abstract":"Diabetes is accompanied by inflammation and oxidation. Supplementation of anti-inflammatory and antioxidant compounds can prevent the progression of diabetes. This study aimed to investigate the effects of supplementation of Nannochloropsis oculata microalgae (NOM) on the inflammatory and antioxidant responses in diabetic rats. Sixty male rats were divided into six groups as diabetic and non-diabetic rats receiving 0, 10 and 20 mg/kg of body weight of NOM daily for 21 days. Body weight, the serum concentrations of insulin and glucose and the tissue concentrations of interleukin-1β (IL-1β), tumor necrosis factor-alpha (TNF-α), nuclear factor kappa B (NF-κB), interleukin-6 (IL-6), malondialdehyde (MDA), ferric reducing antioxidant power (FRAP), superoxide dismutase (SOD), glutathione peroxidase (GPx) were assessed. The results showed that induction of diabetes significantly reduced the body weight, the serum concentrations of insulin and the tissue concentrations of SOD, FRAP and GPx while increasing the concentrations of glucose, MDA, IL-1β, IL-6, NF-κB and TNF-α. Daily oral administration of NOM (10 and 20 mg/kg) significantly maintained the body weight, the serum concentrations of insulin and the tissue concentrations of SOD, FRAP and GPx while preventing the increase in the concentrations of glucose, MDA, IL-1β and TNF-α. In conclusion, diabetes caused inflammation and oxidation while NOM worked as a natural anti-inflammatory and antioxidant compound.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"314-321"},"PeriodicalIF":0.0,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40657886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Insights into functional connectivity in mammalian signal transduction pathways by pairwise comparison of protein interaction partners of critical signaling hubs. 通过对关键信号中枢蛋白相互作用伙伴的两两比较，深入了解哺乳动物信号转导途径的功能连接。

IF 2.6

Biomolecular Concepts Pub Date : 2022-09-01 eCollection Date: 2022-01-01 DOI: 10.1515/bmc-2022-0023

Chilakamarti V Ramana

{"title":"Insights into functional connectivity in mammalian signal transduction pathways by pairwise comparison of protein interaction partners of critical signaling hubs.","authors":"Chilakamarti V Ramana","doi":"10.1515/bmc-2022-0023","DOIUrl":"10.1515/bmc-2022-0023","url":null,"abstract":"Growth factors and cytokines activate signal transduction pathways and regulate gene expression in eukaryotes. Intracellular domains of activated receptors recruit several protein kinases as well as transcription factors that serve as platforms or hubs for the assembly of multi-protein complexes. The signaling hubs involved in a related biologic function often share common interaction proteins and target genes. This functional connectivity suggests that a pairwise comparison of protein interaction partners of signaling hubs and network analysis of common partners and their expression analysis might lead to the identification of critical nodes in cellular signaling. A pairwise comparison of signaling hubs across several related pathways might reveal novel signaling modules. Analysis of protein interaction connectome by Venn (PIC-Venn) of transcription factors STAT1, STAT3, NFKB1, RELA, FOS, and JUN, and their common interaction network suggested that BRCA1 and TSC22D3 function as critical nodes in immune responses by connecting the signaling hubs into signaling modules. Transcriptional regulation of critical hubs may play a major role in the lung epithelial cells in response to SARS-CoV-2 and in COVID-19 patients. Mutations and differential expression levels of these critical nodes and modules in pathological conditions might deregulate signaling pathways and their target genes involved in inflammation. Biological connectivity emerges from the structural connectivity of interaction networks across several signaling hubs in related pathways. The main objectives of this study are to identify critical hubs, critical nodes, and modules involved in the signal transduction pathways of innate and adaptive immunity. Application of PIC-Venn to several signaling hubs might reveal novel nodes and modules that can be targeted by small regulatory molecules to simultaneously activate or inhibit cell signaling in health and disease.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"298-313"},"PeriodicalIF":2.6,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40336732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oxygen diffusion pathways in mutated forms of a LOV photoreceptor from Methylobacterium radiotolerans: A molecular dynamics study. 放射耐受甲基杆菌LOV光感受器突变形式中的氧扩散途径:分子动力学研究。

Biomolecular Concepts Pub Date : 2022-03-25 DOI: 10.1515/bmc-2022-0013

Rocco Zerlotti, Aba Losi, Eugenia Polverini

{"title":"Oxygen diffusion pathways in mutated forms of a LOV photoreceptor from Methylobacterium radiotolerans: A molecular dynamics study.","authors":"Rocco Zerlotti, Aba Losi, Eugenia Polverini","doi":"10.1515/bmc-2022-0013","DOIUrl":"https://doi.org/10.1515/bmc-2022-0013","url":null,"abstract":"Mr4511 from Methylobacterium radiotolerans is a photoreceptor of the light, oxygen voltage (LOV) family, binding flavin mononucleotide (FMN) as a chromophore. It exhibits the prototypical LOV photocycle, with the reversible formation of an FMN-Cys71 adduct via fast decay of the FMN triplet state. Mr4511 has high potential as a photosensitiser for singlet oxygen (SO) upon mutation of C71. Mr4511-C71S shows a triplet lifetime (τ T) of several hundreds of microseconds, ensuring efficient energy transfer to dioxygen to form SO. In this work, we have explored the potential diffusion pathways for dioxygen within Mr4511 using molecular dynamics (MD) simulations. The structural model of wild-type (wt) Mr4511 showed a dimeric structure stabilised by a strong leucine zipper at the two C-terminal helical ends. We then introduced in silico the C71S mutation and analysed transient and persistent oxygen channels. MD simulations indicate that the chromophore binding site is highly accessible to dioxygen. Mutations that might favour SO generation were designed based on their position with respect to FMN and the oxygen channels. In particular, the C71S-Y61T and C71S-Y61S variants showed an increased diffusion and persistence of oxygen molecules inside the binding cavity.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"164-174"},"PeriodicalIF":0.0,"publicationDate":"2022-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40328291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Calcium signaling in prostate cancer cells of increasing malignancy. 恶性程度增加的前列腺癌细胞中的钙信号。

Biomolecular Concepts Pub Date : 2022-03-24 DOI: 10.1515/bmc-2022-0012

Carla Marchetti

{"title":"Calcium signaling in prostate cancer cells of increasing malignancy.","authors":"Carla Marchetti","doi":"10.1515/bmc-2022-0012","DOIUrl":"https://doi.org/10.1515/bmc-2022-0012","url":null,"abstract":"Calcium signaling controls a large variety of cell functions, including proliferation and apoptosis, and plays a major role in neoplastic transformation. Prostate cancer (PCa) is one of the most common malignancies in men. The transition to castration-resistant prostate cancer (CRPC), a lethal form that is still lacking an effective cure, could be influenced by fine tuning intracellular calcium ([Ca2+]i) homeostasis. This study investigates [Ca2+]i dynamics in metastatic PCa cell lines that mimic the progression of PCa to CRPC: (i) well differentiated LNCaP cells that require androgen for survival, and (ii) poorly differentiated, highly aggressive androgen-insensitive prostate cancer (AIPC) PC3 and DU145 cells. In AIPC cells, ATP induces a fast rise in [Ca2+]i, due to release from intracellular stores and sensitive to phospholipase C inhibitors, while LNCaP cells do not respond to ATP challenge. Moreover, AIPC cells showed a reduced capacity to store Ca2+ in thapsigargin-sensitive stores and limited store-operated calcium entry, with respect to androgen-dependent LNCaP cells. Finally, green tea extract causes [Ca2+]i elevation and inhibits proliferation in PC3 and DU145 cells, but is ineffective in LNCaP cells. The consequences of these differences are discussed and interpreted in this study with reference to previously proposed models for Ca2+ dependence of prostate carcinogenesis.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"156-163"},"PeriodicalIF":0.0,"publicationDate":"2022-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40327339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Calorimetry of extracellular vesicles fusion to single phospholipid membrane. 细胞外囊泡与单磷脂膜融合的量热法。

Biomolecular Concepts Pub Date : 2022-03-21 DOI: 10.1515/bmc-2022-0011

Miriam Grava, Sally Helmy, Mario Gimona, Pietro Parisse, Loredana Casalis, Paola Brocca, Valeria Rondelli

{"title":"Calorimetry of extracellular vesicles fusion to single phospholipid membrane.","authors":"Miriam Grava, Sally Helmy, Mario Gimona, Pietro Parisse, Loredana Casalis, Paola Brocca, Valeria Rondelli","doi":"10.1515/bmc-2022-0011","DOIUrl":"https://doi.org/10.1515/bmc-2022-0011","url":null,"abstract":"Extracellular vesicles (EVs)-mediated communication relies not only on the delivery of complex molecular cargoes as lipids, proteins, genetic material, and metabolites to their target cells but also on the modification of the cell surface local properties induced by the eventual fusion of EVs' membranes with the cells' plasma membrane. Here we applied scanning calorimetry to study the phase transition of single phospholipid (DMPC) monolamellar vesicles, investigating the thermodynamical effects caused by the fusion of doping amounts of mesenchymal stem cells-derived EVs. Specifically, we studied EVs-induced consequences on the lipids distributed in the differently curved membrane leaflets, having different density and order. The effect of EV components was found to be not homogeneous in the two leaflets, the inner (more disordered one) being mainly affected. Fusion resulted in phospholipid membrane flattening associated with lipid ordering, while the transition cooperativity, linked to membrane domains' coexistence during the transition process, was decreased. Our results open new horizons for the investigation of the peculiar effects of EVs of different origins on target cell membrane properties and functionality.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"148-155"},"PeriodicalIF":0.0,"publicationDate":"2022-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40308019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Diagnostic accuracy of genetic markers for identification of the Lr46/Yr29 "slow rusting" locus in wheat (Triticum aestivum L.). 小麦Lr46/Yr29“慢锈”位点遗传标记的诊断准确性

Biomolecular Concepts Pub Date : 2022-02-22 DOI: 10.1515/bmc-2022-0002

Roksana Bobrowska, Aleksandra Noweiska, Julia Spychała, Agnieszka Tomkowiak, Jerzy Nawracała, Michał T Kwiatek

{"title":"Diagnostic accuracy of genetic markers for identification of the Lr46/Yr29 \"slow rusting\" locus in wheat (Triticum aestivum L.).","authors":"Roksana Bobrowska, Aleksandra Noweiska, Julia Spychała, Agnieszka Tomkowiak, Jerzy Nawracała, Michał T Kwiatek","doi":"10.1515/bmc-2022-0002","DOIUrl":"https://doi.org/10.1515/bmc-2022-0002","url":null,"abstract":"Wheat leaf rust, caused by fungal pathogen Puccinia triticina Erikss, annually contributes to production losses as high as 40% in susceptible varieties and remains as one of the most damaging diseases of wheat worldwide. Currently, one of the major challenges of wheat geneticists and breeders is to accumulate major genes for durability of rust resistance called \"slow rusting\" genes using marker-assisted selection (MAS). Until now, eight genes (Lr34/Yr18, Lr46/Yr29, Lr67/Yr46, Lr68, Lr74, Lr75, Lr77, and Lr78) conferring resistance against multiple fungal pathogens have been identified in wheat gene pool and the molecular markers were developed for them. In MAS practice, it is a common problem that cultivars exhibiting desirable marker genotypes may not necessarily have the targeted genes or alleles and vice versa, which is known as \"false positives.\" The aim of this study was to compare the available four markers: Xwmc44, Xgwm259, Xbarc80, and csLV46G22 markers (not published yet), for the identification of the Lr46/Yr29 loci in 73 genotypes of wheat, which were reported as sources of various \"slow rusting\" genes, including 60 with confirmed Lr46/Yr29 gene, reported in the literature. This research revealed that csLV46G22 together with Xwmc44 is most suitable for the identification of resistance allele of the Lr46/Yr29 gene; however, there is a need to clone the Lr46/Yr29 loci to identify and verify the allelic variation of the gene and the function.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2022-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39960200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Effect of omega-3 fatty acids on the telomere length: A mini meta-analysis of clinical trials. omega-3脂肪酸对端粒长度的影响:临床试验的小型荟萃分析。

Biomolecular Concepts Pub Date : 2022-02-21 DOI: 10.1515/bmc-2021-0024

Sawan Ali, Giovanni Scapagnini, Sergio Davinelli

{"title":"Effect of omega-3 fatty acids on the telomere length: A mini meta-analysis of clinical trials.","authors":"Sawan Ali, Giovanni Scapagnini, Sergio Davinelli","doi":"10.1515/bmc-2021-0024","DOIUrl":"https://doi.org/10.1515/bmc-2021-0024","url":null,"abstract":"Telomeres are protective caps at the end of eukaryotic chromosomes, whose length is correlated with health and lifespan. Telomere attrition is a common feature of the aging process and can be accelerated by oxidative stress and chronic inflammation. Various nutrients influence the telomere length, partially due to their antioxidant and anti-inflammatory properties. The aim of this review was to meta-analytically assess the effect of omega-3 fatty acids on the telomere length. We searched four databases (PubMed, Web of Sciences, Scopus, and the Cochrane Library) from inception until November 2021. Of 573 records, a total of 5 clinical trials were included for the quantitative meta-analysis, comprising a total of 337 participants. The results revealed an overall beneficial effect of omega-3 fatty acids on the telomere length (mean difference = 0.16; 95% CI, 0.02, 0.30; p = 0.02). Despite a limited number of studies, the available evidence suggests that omega-3 fatty acids may positively affect the telomere length. However, larger clinical trials are needed to confirm our findings, along with studies aimed to clarify the underlying molecular mechanisms.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"25-33"},"PeriodicalIF":0.0,"publicationDate":"2022-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39942342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Analysis of differentially expressed genes and signaling pathways involved in atherosclerosis and chronic obstructive pulmonary disease. 动脉粥样硬化和慢性阻塞性肺疾病的差异表达基因和信号通路分析。

Biomolecular Concepts Pub Date : 2022-02-21 DOI: 10.1515/bmc-2022-0001

Stanislav Kotlyarov

{"title":"Analysis of differentially expressed genes and signaling pathways involved in atherosclerosis and chronic obstructive pulmonary disease.","authors":"Stanislav Kotlyarov","doi":"10.1515/bmc-2022-0001","DOIUrl":"https://doi.org/10.1515/bmc-2022-0001","url":null,"abstract":"Atherosclerosis is an important medical and social problem, and the keys to solving this problem are still largely unknown. A common situation in real clinical practice is the comorbid course of atherosclerosis with chronic obstructive pulmonary disease (COPD). Diseases share some common risk factors and may be closely linked pathogenetically.Methods: Bioinformatics analysis of datasets from Gene Expression Omnibus (GEO) was performed to examine the gene ontology (GO) of common differentially expressed genes (DEGs) in COPD and peripheral arterial atherosclerosis. DEGs were identified using the limma R package with the settings p < 0.05, corrected using the Benjamini & Hochberg algorithm and ǀlog 2FCǀ > 1.0. The GO, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and the protein-protein interaction (PPI) network analysis were performed with the detected DEGs.Results: The biological processes and signaling pathways involving common DEGs from airway epithelial datasets in COPD and tissue in peripheral atherosclerosis were identified. A total of 15 DEGs were identified, comprising 12 upregulated and 3 downregulated DEGs. The GO enrichment analysis demonstrated that the upregulated hub genes were mainly involved in the inflammatory response, reactive oxygen species metabolic process, cell adhesion, lipid metabolic process, regulation of angiogenesis, icosanoid biosynthetic process, and cellular response to a chemical stimulus. The KEGG pathway enrichment analysis demonstrated that the common pathways were Toll-like receptor signaling pathway, NF-kappa B signaling pathway, lipid and atherosclerosis, and cytokine-cytokine receptor interaction.Conclusions: Biological processes and signaling pathways associated with the immune response may link the development and progression of COPD and atherosclerosis.","PeriodicalId":38392,"journal":{"name":"Biomolecular Concepts","volume":" ","pages":"34-54"},"PeriodicalIF":0.0,"publicationDate":"2022-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39942344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6